mMO151_MFTAv2.2_mouse_final.RDS

The goal of this work is to identify mouse receptors that are ideally specific, or at least enriched in mMO germ cells

In the analysis below, we:
Read in the mMO151_MFTAv2.2_mouse_final.RDS and either germ = Yes or germ = No Attempted to run DGE analysis (fit_models()) on a downsampled atlas + entire mMO cds However, this led to memory issues. Moving forward I ran DGE analysis using just the mMO subset. The DGE results were filtered to only considered genes that are present in the mouse receoptors list. Finally, results were filtered by lFC (estimate) and q_value (corrected p-value) and plotted for visualization.

We find there are two datasets in this cds, Invitro and MFTAv2.2. They are well mixed asside from immune / endothelial cell calls.

To identify germ enriched genes. We first define a variable “germ” and assign cells either Yes or No Depending on whether their assigned_cell_type / partition belongs to PGC/germ. Now we run DGE analysis. Attempts to include a down-sampled portion of the MFTAv2.2 and run DGE analysis on a combined object continually hit memory limit issues. However, because the datasets are well mixed, and becasue the InVitro subset itself has thousands of cells it is reasonable to run DGE analysis on just the InVitro subset.

After DGE analysis, we filter by lfc >3 and q_value < 0.05. Next, we subset the results to only consider genes identified as mouse receptors. Finally, we plot the results. We can see that Tex101 is a good candidate for a receptor/surface marker that is predominantly expressed in the PGC/Germ compartment. Other candidates have similar enrichment/specificity, but much lower relative expression.